Den 2020-03-28 kl. 04:01, skrev Guilherme Carneiro Queiroz da Silva:
Hi all,
I look on google for any answers for such question in this maillist, and I
found related questions but no final answer.
I wish to compute the heat flux for my system using GK relations. I found the
gromacs extension force the calculation of the per atom stress
(http://www.mdstress.org/index.php/mdstresslib/). However, it still lacks the
per atom energies. Did someone manage to extract such properties?
I'm aware i could use enemat but had to do a large numbers of reruns in order
to cover each atom obeying the group limit of gromacs, since this could be
tedious I'm looking for other solutions. Could editing the trajectory code in
order to extract not only forces but also the energies be the only solution?
The reason that there is no support is that it is not physically
meaningful, at least not to my knowledge. How would you partition the
bond energy in a HCl molecule into atoms?
In an isolated system it is in principle possible to compute interaction
energies, using the typical pair potentials that classical force fields
apply. However, these force fields ignore higher order interactions,
which means this is a crude approximation.
In a periodic system the computation of energies and energy components
is even more cumbersome, although we have attempted that using potential
of mean force calculation in JCTC 9 pp. 4542-4551 (2013).
Thanks for any help,
Guilherme Carneiro
mdStress.org :: MDStressLib<http://www.mdstress.org/index.php/mdstresslib/>
MDStress Library. MDStressLib is a standalone C++ library developed for local
stress calculations. This library can be integrated into any molecular
simulation code to compute local stress fields in 3D.
www.mdstress.org
--
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se
--
Gromacs Users mailing list
* Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
* Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
* For (un)subscribe requests visit
https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a
mail to gmx-users-requ...@gromacs.org.
